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ECS 5 – 5th European Crystallographic School

5th European Crystallographic School

8 - 14 July 2018

Welcome to Stellenbosch!

Dear Colleagues, we are pleased to invite you and your students to attend the 5th European Crystallographic School to be held in Stellenbosch, South Africa, 8-14 July 2018 under the auspices of the European Crystallographic Association, International Union of Crystallography and the South African Crystallographic Society.

The aim of the school is to give attendees a fundamental understanding of the principles underpinning crystallography through a combination of lectures and hands-on tutorials. We will begin by covering the basic principles of point groups, space groups, crystallisation, data collection, and structure refinement from a theoretical perspective. Thereafter, participants will separate into two groups to apply this knowledge to either biological crystallography or materials science.


The school will be held on the picturesque campus of Stellenbosch University, which is situated in the heart of the historical town of Stellenbosch, a popular tourist destination surrounded by mountains and vineyards. It is well-known for the excellent locally-produced wine, good food and a range of modern art galleries. Also nearby is Cape Town, a vibrant, cosmopolitan city world renowned for the iconic Table Mountain and beautiful beaches inhabited by penguins!

We look forward to welcoming you to Stellenbosch in 2018.


Best wishes,

Catharine Esterhuysen

(on behalf of the ECS5 Organising Committee)


The 5th European Crystallographic School will be held on the campus of Stellenbosch University, which situated in the centre of the town, utilising its state-of-the-art lecturing and X-ray diffraction facilities. Stellenbosch, affectionately known as the Town of Oaks or “Eikestad”, is nestled at the foothills of the Jonkershoek and Simonsberg Mountains which is the source to the Eerste (First) River that winds its way through the town. The documented history of Stellenbosch dates back to 1679 when farmland was developed to supply food to the settlers in Cape Town. Today, Stellenbosch is a bustling town in the heart of the Winelands, with a unique character where a strong historical atmosphere is combined with the advances of a modern society. Stellenbosch University, with more than 24 000 students, also provides a robust educational character to the town. Stellenbosch is a mere 25 minutes away from Cape Town International Airport and 45 minutes from the centre of Cape Town.


Very basic dormitory-style accommodation (including breakfast) in a Stellenbosch University residence has been arranged for 8 – 14 July 2018. Cost: R 2 100 If you will be arriving earlier or staying later than these dates, or should you wish to stay in one of the many good hotels or guest houses in the area, you will have to arrange your accommodation yourself.
The terms and conditions for this accommodation can be found here. -


Stellenbosch can be easily explored on foot, offering a variety of charming shops, galleries, curio shops and restaurants. It is situated in a valley (average elevation of 136m) at the foot of the Cape Fold mountain range and is surrounded by mountains reaching more than 1,500 m. Visitors who have more time to spend will find that Stellenbosch provides a base from which to explore the Cape region. Regarding agricultural activities it is best known for grape and wine production, being part of the Cape Winelands, as the Mediterranean climate with hot dry summers and cool winters is excellent for grape production. The Western Cape area itself is one of the most important horticultural regions in South Africa, with 52,300 ha of fruit trees under cultivation and the majority of the country’s apple, pear and stone fruit production being situated in this area. The Cape Peninsula with its beautiful beaches and nature reserves and vibrant Cape Town are also easily accessible from Stellenbosch. This region is a biodiversity hotspot and features many protected areas with a high level of endemism for both fauna and flora.

Stellenbosch University

Stellenbosch University is home to around 30 000 students and 3 000 staff members (of which 1 000 are academics) spread over five campuses. The high quality of teaching and research, state-of-art facilities and beauty of the campus has attracted students and staff from around 100 countries, strengthening its position as one of the top 300 universities in the world according to the Times Higher Education World University Rankings. Stellenbosch University is one of the oldest universities in South Africa, and in 2018 the Faculty of Science will be celebrating its centenary.

Discover Stellenbosch University

Stellenbosch University started as a Theological College in the mid-nineteenth century, yielding an architectural legacy of that contributes to the beauty of the Stellenbosch campus. The aesthetics of the campus has been carefully considered in the design of new buildings, to the extent that the JS Gericke library was built underground to maintain the open character of the Jan Marais square, which is surrounded by historical red-roofed buildings.


There are many national and international flights that arrive daily at Cape Town International airport from a variety of destinations. Free transport between Cape Town International Airport and Stellenbosch will be offered by the organisers on 8 and 14 July only. Should you be arriving earlier or leaving later please arrange your own transport to Stellenbosch. The easiest is by rental car: The better known rental companies have pick-up points in the airport. Ensure that you have made arrangements prior to arrival. Directions: From Cape Town International airport take the N2 towards Somerset West. Turn left onto the R310 and follow the road into Stellenbosch. From Cape Town take the N1 in a northerly direction and turn off at Exit 39 onto the R304 and follow through into Stellenbosch.
A map of the campus can be found here. -


ECS5 2018 brings an exciting range of experience to the school.


Below is the program for ECS5 2018.

08:00 - 12:30

12:30 - 13:45

13:45 - 14:00

Susan Bourne (UCT)

Symmetry operations and their combination in crystals, i.e. the 32 crystallographic point groups will be discussed.

15:30 - 16:00

Gert Kruger (UJ)

The unit cell, the smallest repeating unit of the crystal structure, and the arrangement of the atoms/molecules/ions in the lattice points of the crystalline material will be discussed. The 14 Bravais lattices will be denoted.

8:30 - 9:00



Luigi Nassimbeni (UCT)

The formation of the 230 crystallographic space groups, as the result of the combination of 14 Bravais lattices with 32 point groups when translational symmetry elements are included, will be discussed.

10:30-11:00 AM

11:00-12:30 PM

Andrew Bond (UCambridge)

Scattering of X-rays on a crystal lattice and its mathematical description (Fourier transformation, scattering factor calculations, and reciprocal lattice) will be discussed.

12:30-14:00 PM

14:00-15:30 PM

Ilia Guzei (UW-M)

General instrumentation will be described: anatomy of a modern diffractometer, radiation sources, beam optics and detectors.

15:30-16:00 PM

16:00-17:30 PM

Niki Báthori (CPUT)

Procedures are often used to prepare single crystals suitable for structure determination by X-ray crystallography will be discussed.

17:30-18:00 PM

8:30-9:00 AM

9:00-10:30 AM

Manuel Fernandes (Wits) and Tobias Stürzer (Bruker)

Recording the diffraction pattern (i.e. measuring the intensity and angle of diffracted X-rays), indexing, integration and scaling of data will discussed. Resolution limits, target values of completeness and redundancy will be critically assessed.

10:30-11:00 AM

11:00-12:30 PM

Andrew Bond (UCambridge)

Structure solution is the process of obtaining accurate phases in order to build a molecular model. General structure solution methods (direct methods, Patterson function) will be discussed.

12:30-14:00 PM

Ilia Guzei (UW-M)

Aspects of importance to structure refinement, in particular thermal motion, convergence, R-factors and goodness of fit.

15:30-16:00 PM

16:00-17:30 PM

17:30-18:00 PM

8:30-9:00 AM

Wolf-Dieter Schubert (UP)

During this lecture, students will be familiarized with the properties and origin of proteins. They will learn how proteins are isolated from original sources or heterologously produced in various production systems. They will then learn the principles that are applied in isolating and purifying proteins. A third aspect will be to learn how proteins may be induced to form regular, three-dimensional arrays or crystals.

Delia Haynes (UStell)

Crystallographic databases as the repositories of huge amounts of useful crystallographic data will be discussed, with particular focus on the Cambridge Structural Database for small molecules.

10:30-11:00 AM

Wolf-Dieter Schubert (UP) and Kofi Boafoh (UP)

During this practical session, students will set up crystallization plates with lysozyme by sitting and hanging drop.

Ilia Guzei (UW-M)

Introduction to XPREP and OLEX2.

12:30-18:00 PM

8:30-9:00 AM

Serah Kimani (UCT)

During this lecture, students will learn about the critical factors in obtaining complete diffraction data from macromolecular crystals to as high a resolution as possible. The principles behind evaluating diffraction images and converting the data to tables of reflections will be explained. In addition, the nature of these reflections will be discussed.

Andrew Bond (UCambridge), Ilia Guzei (UW-M) and Leigh Loots (UStell)

Practical examples of solving and refining routine structures will be covered with hands-on experience.

10:30-11:00 AM

Andrew Bond (UCambridge) and Ilia Guzei (UW-M); Leigh Loots (UStell)

Practical examples of solving and refining routine structures will be covered with hands-on experience.

Tobias Krojer (UOxford)

During this lecture, students will be taught the principles of solving protein structures from diffraction data will be illustrated. The limitations of diffraction experiments will be outlined and how these can be overcome.

12:30-14:00 PM

Serah Kimani (UCT), Jeremy Woodward (UCT), Kofi Boafoh (UP)

This will be a practical session at the University of Cape Town, where diffraction data will be collected – ideally from crystals grown by students of the course.

Dave Billing (Wits)

Powder X-ray diffraction is an important technique in the characterization, identification and quantification of materials in the solid state. The course will include the following topics: an introduction to PXRD diffraction physics, instrumentation (different geometries), the interpretation of profiles (basic phase identification), common pitfalls (preferred orientation, sample size, etc.), particle size analysis and if time permits, an introduction to Rietveld (and /or Pawley) refinement.

15:30-16:00 PM

Tobias Krojer (UOxford), Jeremy Woodward (UCT), Serah Kimani (UCT)

Diffraction data sets collected on the diffractometer during the previous session will be used to solve the structure either by using anomalous data or by molecular replacement.

Dave Billing (Wits)

These two session will build on the topics introduced in the previous session (MS5); they will extend Rietveld method to structure solution and refinement. If time permits, it will expand on Pawley and le Bail whole pattern methods for phase purity analysis. In the hands-on tutorial session attendees will be introduced to the use of single-crystal X-ray diffraction data and the CSD (calculation of PXRD traces, preferred orientation tool, etc.) in the interpretation of PXRD profiles.

17:30-18:00 PM

8:30-9:00 AM

Sylvia Fannucchi (WITS)

Students will learn about the principles of protein structure refinement, how to find potential errors in their protein structures and how to analyse a protein structure in general.

Varia Nikolayenko (US), Manuel Fernandes (Wits), Vincent Smith (Rhodes)

MS7 will focus on single-crystal X-ray diffraction data collection under gas pressure and variable temperature. This section will include information on setting up data collection protocols and data quality assessment.

10:30-11:00 AM

Jeremy Woodward (UCT)

The structural analysis of biological macromolecules – and especially of large complexes – is currently undergoing a revolution through the dramatic improvement of cryo-electron microscopy of biological samples. The underlying principles and the applicability of the technique will be discussed.

12:30-14:00 PM

Wolf-Dieter Schubert (UP)

Students will be shown how to make use of the information in the Protein Data Bank for their own projects and potentially how to generate models of proteins where a crystal structure is not yet available.

Clive Oliver (UCT) and Vincent Smith (Rhodes)

This section will deal with disorder and twinning. It will introduce advanced coding in ShelX, identification of disorder (signs that your structure may be disordered), identification of the type of disorder (static or dynamic), and how to go about modelling the disorder. It will also introduce the program SQUEEZE (ex PLATON) and the conditions of its application to structures that contain disorder (why and when to use it). We will also cover the very basics of twinning, warning signs, types of twinning, choosing appropriate strategies, and the tools used to model the twinning.

15:30-16:00 PM

Sylvia Fannucchi (WITS), Jeremy Woodward (UCT), Kofi Boafoh (UP)

Students will be able to build complete protein models, refine these models and iteratively improve on the models. They will also be able to assess the quality of their crystals structure and investigate the relevance of their crystal structure.

17:30-18:00 PM

18:30 PM

8:30-9:00 AM

9:00-10:30 AM

Clive Oliver (UCT)

Preparing results for publication will be described here, in particular, preparation of CIF files, describing structures and what to consider for molecular graphics.

10:30-11:00 AM

André Roodt (UFS)

An overview of how crystallographic information can be used to understand properties of compounds for application in fields such as the petrochemical, medical and metal beneficiation industries and the environment.

Unless otherwise indicated the venue for all lectures is room 1015 in the First Year Chemistry building – building 56 on the Stellenbosch University Campus Map:


Organising Committee

ESC5 2018 is made possible through the dedication of the following organisers:


Find all your electronic material right here!


Our main sponsors


Should you have any questions about the school, please feel to correspond via our workshop email: mdp@sun.ac.za or telephone +27 (0)21 808 3347.